# License
^LICENSE\.md$

# IDE
^\.vscode$
^\.Rproj\.user$
^.*\.Rproj$

# Version control
^\.git$
^\.github$
^\.gitignore$

# Python package files (keep separate from R package)
^src$
^CMakeLists\.txt$
^pyproject\.toml$
^setup\.py$
^MANIFEST\.in$

# Build artifacts
^build
^dist
^_build
^\.pixi
^pixi\.lock$
^\.pytest_cache
^__pycache__
^\.mypy_cache
^\.ruff_cache

# Conda
^conda-build$

# Documentation (keep R vignettes, exclude Python docs)
^docs$
^\.readthedocs\.yaml$

# Test files (keep R tests, exclude Python tests)
^tests/test_.*\.py$
^tests/.*\.c$
^pytest\.ini$

# Markdown documentation files (keep vignettes, exclude dev docs)
^PHASE.*\.md$
^R_API_IMPLEMENTATION\.md$
^R_API_TEST_RESULTS\.md$
^R_API_FINAL_TEST_REPORT\.md$
^R_INSTALLATION_GUIDE\.md$
^R_PACKAGE_SUMMARY\.md$
^CONDA_INSTALLATION\.md$
^R_PACKAGE_INSTALLATION_CHECK\.md$

# R test scripts
^test_.*\.R$
^install_r_package\.R$

# CRAN submission
^cran-comments\.md$

# Non-standard top-level files
^CLAUDE\.md$
^DEVEL\.md$
^examples$
^hierarchical_cache$
^include$
^LICENSE\.txt$
^Makefile$
^paper\.pdf$
^phasic\.pc\.in$
^phasiccpp\.pc\.in$
^R_API_COMPLETE_TEST_SUMMARY\.md$
^R_BUILD_TEST_RESULTS\.md$
^R_LICENSE$
^R_PACKAGE_BUILD_SUMMARY\.md$
^requirements\.txt$
^sandbox$
^scripts$
^test$
^utils$
^verify_correctness\.py$
^README\.md$
^NEWS\.md$

# API directories and headers
^api$
^include$

# Data cache
^\.phasic_cache$

# Development files
^\.claude
^\.devcontainer
^\.scripts
^debug
^\.DS_Store
^hybrid-p2p-dist
